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The present study proposes a new quadrature orthogonal signal correlation (QOSC) filtering method based on principal component analysis (PCA). The external perturbation variable vector typically used in the QOSC operation is replaced with a matrix consisting of the spectral data principal components (PCs) and their quadrature counterparts obtained by using the discrete Hilbert-Noda transformation. Thus, QOSC operation can be carried out for a dataset without the explicit knowledge of the external variables information. The PCA-based QOSC filtering can be most effectively applied to two-dimensional (2D) correlation analysis. The performance of this filtering operation on the simulated spectra data set with the interference of strong random noise demonstrated that the PCA-based QOSC filtering not only eliminates the influence of signals that are unrelated to the final target but also preserves the out-of-phase information in the data matrix essential for asynchronous correlation analysis. The result of 2D correlation analysis has also demonstrated that essentially only one principal component is necessary for PCA-based QOSC to perform well. Although the present PCA-based QOSC filtering scheme is not as powerful as that based on the explicit knowledge of the external variable vector, it still can significantly improve the quality of 2D correlation spectra and enables OSC 2D to deal with the problems of losing the quadrature (or out-of-phase) information. In particular, it opens a way to perform QOSC for the spectral dataset without external variables information. The proposed approach should have wide applications in 2D correlation analysis of spectra driven by multiplicative effects in complicated systems in biological, pharmaceutical, and agriculture fields, and so on, where the explicit nature of the external perturbation cannot always be known.